I wouldn’t go so far as to qualify mitochondria as a separate species, but there are certainly some (e.g., Lynn Margulis) who believe the origins of eukaryotes can be traced to just such a primeval symbiosis:
Mitochondria certainly were a separate species a long time ago, before they colonized primitive eukaryotic cells. The endosymbiotic origin of mitochondria and certain other organelles has been extremely well established in recent years. (Note that the cites above are from 1981, and things have changed drastically since then. Margulies wrote all that before the advent of molecular phylogenetic analysis, which gives very powerful additional evidence for the endosymbiotic model.)
But it’s been an extremely long time since we entered into this symbiotic relationship with mitochondria, and most of the proteins they need to function are now encoded by the nuclei of the cells they inhabit. Biologists consider mitochondria now just to be part of eukaryotic cells, and not a separate species.
Note, though, that “species” is an artificial concept, and the answer to a question like this, and a lot of other questions about species, is often going to be a matter of opinion.